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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgggttggttatagaatctcatgtagaattgctctttttcatctggtcattctgatgactgaaatctgtatctgacatatggtatcctgttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGATTGCTGAGATGAGCTCTGAGAGTGGGGAGGCTGCAATACAGAAACTACAA

Basic information

species Vitis vinifera
transcript Vv06s0004g00950.t01
intron # 17
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|27580831|gb|CB003526.1|CB003526
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACNATGAAAG                         AAGTGAGAGGCTGAAGCTG
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTG
EST: gi|110362164|gb|EC925680.1|EC925680
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAG                         AAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
EST: gi|32249956|gb|CD715775.1|CD715775
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAG                         AAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
EST: gi|110370378|gb|EC929549.1|EC929549
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAG                         AAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
EST: gi|27579894|gb|CB002589.1|CB002589
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAG                         AAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
EST: gi|27581325|gb|CB004020.1|CB004020
EST:     CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAG                         AAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT
genomic: CAGATCCAGCGGAAAAAGGAGGAAGTTCAAATGGAATTGGACAATGAAAGgtgcttttcc ... gttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcattctgatgactgaaatctgtatctgacatatggtatcctgttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGATTGCTGAGATGAGCTCTGAGAGTGGGGAGGCTGCAATACAGAAACTACAA
                          atctgac  putative branch site (score: 3)
                                         tcctgtt  putative PPT
                                              ttaaacta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgggttggttatagaatctcatgtagaattgctctttttcatctggtcattctgatgactgaaatctgtatctgacatatggtatcctgttaaactagAAGTGAGAGGCTGAAGCTGGAAGAAGAGCTGAAGGAATTGAATAGGGAGATTGCTGAGATGAGCTCTGAGAGTGGGGAGGCTGCAATACAGAAACTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- -gggttgg
- - - - - - - - - - tcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgacat